[2024-01-25 19:37:06,038] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:37:06,039] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:37:06,040] [INFO] DQC Reference Directory: /var/lib/cwl/stg92afb36c-4aec-49e1-8f8e-791458188d4e/dqc_reference
[2024-01-25 19:37:07,195] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:37:07,196] [INFO] Task started: Prodigal
[2024-01-25 19:37:07,196] [INFO] Running command: gunzip -c /var/lib/cwl/stgce612a2e-0c7c-4f9e-90ce-a56194c1ad1f/GCF_003028415.1_ASM302841v1_genomic.fna.gz | prodigal -d GCF_003028415.1_ASM302841v1_genomic.fna/cds.fna -a GCF_003028415.1_ASM302841v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:37:18,143] [INFO] Task succeeded: Prodigal
[2024-01-25 19:37:18,144] [INFO] Task started: HMMsearch
[2024-01-25 19:37:18,144] [INFO] Running command: hmmsearch --tblout GCF_003028415.1_ASM302841v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92afb36c-4aec-49e1-8f8e-791458188d4e/dqc_reference/reference_markers.hmm GCF_003028415.1_ASM302841v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:37:18,390] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:37:18,392] [INFO] Found 6/6 markers.
[2024-01-25 19:37:18,424] [INFO] Query marker FASTA was written to GCF_003028415.1_ASM302841v1_genomic.fna/markers.fasta
[2024-01-25 19:37:18,424] [INFO] Task started: Blastn
[2024-01-25 19:37:18,424] [INFO] Running command: blastn -query GCF_003028415.1_ASM302841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92afb36c-4aec-49e1-8f8e-791458188d4e/dqc_reference/reference_markers.fasta -out GCF_003028415.1_ASM302841v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:19,025] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:19,029] [INFO] Selected 15 target genomes.
[2024-01-25 19:37:19,029] [INFO] Target genome list was writen to GCF_003028415.1_ASM302841v1_genomic.fna/target_genomes.txt
[2024-01-25 19:37:19,041] [INFO] Task started: fastANI
[2024-01-25 19:37:19,041] [INFO] Running command: fastANI --query /var/lib/cwl/stgce612a2e-0c7c-4f9e-90ce-a56194c1ad1f/GCF_003028415.1_ASM302841v1_genomic.fna.gz --refList GCF_003028415.1_ASM302841v1_genomic.fna/target_genomes.txt --output GCF_003028415.1_ASM302841v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:37:35,840] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:35,841] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92afb36c-4aec-49e1-8f8e-791458188d4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:37:35,841] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92afb36c-4aec-49e1-8f8e-791458188d4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:37:35,852] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:37:35,852] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:37:35,852] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Deinococcus arcticus	strain=OD32	GCA_003028415.1	2136176	2136176	type	True	100.0	1324	1327	95	conclusive
Deinococcus aquaedulcis	strain=SYSU M42101	GCA_019693445.1	2840455	2840455	type	True	88.6451	1068	1327	95	below_threshold
Deinococcus multiflagellatus	strain=KACC 19287	GCA_020166415.1	1656887	1656887	type	True	88.4897	1076	1327	95	below_threshold
Deinococcus grandis	strain=ATCC 43672	GCA_001485435.1	57498	57498	type	True	80.6725	746	1327	95	below_threshold
Deinococcus arenae	strain=JCM 31047	GCA_014647995.1	1452751	1452751	type	True	80.4996	752	1327	95	below_threshold
Deinococcus daejeonensis	strain=JCM 16918	GCA_014647175.1	1007098	1007098	type	True	80.4684	746	1327	95	below_threshold
Deinococcus saudiensis	strain=CGMCC 1.15089	GCA_014640655.1	1765963	1765963	type	True	80.4401	750	1327	95	below_threshold
Deinococcus kurensis	strain=KR-1	GCA_009687825.1	2662757	2662757	type	True	80.3633	776	1327	95	below_threshold
Deinococcus soli (ex Cha et al. 2016)	strain=N5	GCA_001007995.1	1309411	1309411	type	True	80.3051	685	1327	95	below_threshold
Deinococcus radiotolerans	strain=JCM 19173	GCA_014647435.1	1309407	1309407	type	True	80.1949	730	1327	95	below_threshold
Deinococcus koreensis	strain=SJW1-2	GCA_002901445.1	2054903	2054903	type	True	80.0038	700	1327	95	below_threshold
Deinococcus gobiensis	strain=I-0	GCA_000252445.1	502394	502394	type	True	79.8388	627	1327	95	below_threshold
Deinococcus metalli	strain=DSM 27521	GCA_014201805.1	1141878	1141878	type	True	79.6248	674	1327	95	below_threshold
Deinococcus phoenicis	strain=1P10ME	GCA_000599865.1	1476583	1476583	type	True	79.4887	586	1327	95	below_threshold
Deinococcus planocerae	strain=XY-FW106	GCA_002869765.1	1737569	1737569	type	True	78.1871	517	1327	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:37:35,854] [INFO] DFAST Taxonomy check result was written to GCF_003028415.1_ASM302841v1_genomic.fna/tc_result.tsv
[2024-01-25 19:37:35,854] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:37:35,854] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:37:35,855] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92afb36c-4aec-49e1-8f8e-791458188d4e/dqc_reference/checkm_data
[2024-01-25 19:37:35,855] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:37:35,897] [INFO] Task started: CheckM
[2024-01-25 19:37:35,897] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003028415.1_ASM302841v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003028415.1_ASM302841v1_genomic.fna/checkm_input GCF_003028415.1_ASM302841v1_genomic.fna/checkm_result
[2024-01-25 19:38:11,628] [INFO] Task succeeded: CheckM
[2024-01-25 19:38:11,629] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:38:11,669] [INFO] ===== Completeness check finished =====
[2024-01-25 19:38:11,669] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:38:11,670] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003028415.1_ASM302841v1_genomic.fna/markers.fasta)
[2024-01-25 19:38:11,670] [INFO] Task started: Blastn
[2024-01-25 19:38:11,670] [INFO] Running command: blastn -query GCF_003028415.1_ASM302841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92afb36c-4aec-49e1-8f8e-791458188d4e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003028415.1_ASM302841v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:12,515] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:12,518] [INFO] Selected 15 target genomes.
[2024-01-25 19:38:12,518] [INFO] Target genome list was writen to GCF_003028415.1_ASM302841v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:38:12,539] [INFO] Task started: fastANI
[2024-01-25 19:38:12,539] [INFO] Running command: fastANI --query /var/lib/cwl/stgce612a2e-0c7c-4f9e-90ce-a56194c1ad1f/GCF_003028415.1_ASM302841v1_genomic.fna.gz --refList GCF_003028415.1_ASM302841v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003028415.1_ASM302841v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:38:28,401] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:28,410] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:38:28,410] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_003028415.1	s__Deinococcus sp003028415	100.0	1324	1327	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009755355.1	s__Deinococcus sp009755355	83.0679	886	1327	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507665.1	s__Deinococcus actinosclerus	80.7065	710	1327	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.26	96.21	0.94	0.94	4	-
GCF_001485435.1	s__Deinococcus grandis	80.6565	748	1327	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.65	95.40	0.88	0.83	5	-
GCF_014648135.1	s__Deinococcus sedimenti	80.5987	739	1327	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198095.1	s__Deinococcus indicus	80.5968	745	1327	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.28	99.28	0.90	0.90	2	-
GCF_002017875.1	s__Deinococcus sp002017875	80.59	769	1327	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.85	96.85	0.84	0.84	2	-
GCF_001007995.1	s__Deinococcus soli	80.3231	681	1327	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.09	98.03	0.94	0.93	3	-
GCF_014647435.1	s__Deinococcus radiotolerans	80.1982	730	1327	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002901445.1	s__Deinococcus koreensis	79.9894	701	1327	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000252445.1	s__Deinococcus gobiensis	79.8506	624	1327	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647055.1	s__Deinococcus aerolatus	79.7019	627	1327	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201805.1	s__Deinococcus metalli	79.6586	669	1327	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000599865.1	s__Deinococcus phoenicis	79.4846	587	1327	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002869765.1	s__Deinococcus planocerae	78.1653	519	1327	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:38:28,412] [INFO] GTDB search result was written to GCF_003028415.1_ASM302841v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:38:28,412] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:38:28,415] [INFO] DFAST_QC result json was written to GCF_003028415.1_ASM302841v1_genomic.fna/dqc_result.json
[2024-01-25 19:38:28,416] [INFO] DFAST_QC completed!
[2024-01-25 19:38:28,416] [INFO] Total running time: 0h1m22s